I am working on a metabarcoding project and am reeeeeally new to the bioinformatics end of things. I want to create a reference database in OBITools3 by doing an in-silico PCR on all vertebrate sequences in Genbank, using my primer set. The OBITools3 tutorial shows how to get EMBL data [https://git.metabarcoding.org/obitools/obitools3/-/wikis/Wolf-tutorial-with-the-OBITools3#7-taxonomic-assignment-of-the-sequences], but not Genbank data. I don't know what the Genbank URI is, and can't seem to find any info about this online. Maybe this is something quite obvious, but I just don't have the experience in this field yet. Any help is much appreciated!
Help info from OBITools3 documentation:
obi build_ref_db -h
usage: obi build_ref_db [-h] [--skip <N>] [--only <N>]
[--taxonomy OBI:TAXOURI] [--no-create-dms]
[--no-progress-bar] [--threshold <THRESHOLD>]
INPUT OUTPUT
positional arguments:
INPUT Data source URI
OUTPUT Data destination URI
optional arguments:
-h, --help show this help message and exit
Restriction to a sub-part options:
Allows to limit analysis to a sub-part of the input
--skip <N> skip the N first sequences
--only <N> treat only N sequences
Input format options for taxonomy:
--taxonomy OBI:TAXOURI
Taxonomy URI
Output options for DMS data:
--no-create-dms Don't create an output DMS if it does not already
exist
Option to deactivate the display of the progress bar:
--no-progress-bar Do not display progress bar
obi build_ref_db specific options:
--threshold <THRESHOLD>, -t <THRESHOLD>
Score threshold as a normalized identity, e.g. 0.95
for an identity of 95%. Default: 0.99.